Multiple sequence alignment - TraesCS6A01G366100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G366100 chr6A 100.000 2947 0 0 1 2947 593930970 593928024 0.000000e+00 5443.0
1 TraesCS6A01G366100 chr6A 81.786 840 94 28 1048 1878 569679082 569678293 0.000000e+00 649.0
2 TraesCS6A01G366100 chr6A 78.436 895 116 48 1398 2254 593992011 593991156 2.030000e-141 512.0
3 TraesCS6A01G366100 chr6A 77.597 799 99 49 1403 2164 594319658 594320413 7.600000e-111 411.0
4 TraesCS6A01G366100 chr6A 78.052 688 94 39 1403 2069 594253863 594253212 5.960000e-102 381.0
5 TraesCS6A01G366100 chr6A 80.984 447 47 26 956 1402 594254308 594253900 1.320000e-83 320.0
6 TraesCS6A01G366100 chr6A 82.653 392 39 14 88 460 594364283 594364664 1.320000e-83 320.0
7 TraesCS6A01G366100 chr6A 81.236 437 44 24 1935 2336 594366509 594366942 4.740000e-83 318.0
8 TraesCS6A01G366100 chr6A 78.947 494 64 24 930 1402 594319147 594319621 1.720000e-77 300.0
9 TraesCS6A01G366100 chr6A 77.994 309 24 22 550 814 594364786 594365094 1.410000e-33 154.0
10 TraesCS6A01G366100 chr6A 84.615 117 10 5 296 409 593776404 593776515 3.110000e-20 110.0
11 TraesCS6A01G366100 chr6A 100.000 30 0 0 867 896 594365111 594365140 4.100000e-04 56.5
12 TraesCS6A01G366100 chr6D 80.782 1509 169 56 464 1904 447214390 447212935 0.000000e+00 1068.0
13 TraesCS6A01G366100 chr6D 82.927 1148 128 29 1050 2163 447761100 447762213 0.000000e+00 972.0
14 TraesCS6A01G366100 chr6D 79.079 760 99 35 678 1417 447279199 447278480 4.450000e-128 468.0
15 TraesCS6A01G366100 chr6D 81.683 606 50 24 34 591 447216494 447215902 5.790000e-122 448.0
16 TraesCS6A01G366100 chr6D 80.282 497 48 25 930 1402 447737623 447738093 2.190000e-86 329.0
17 TraesCS6A01G366100 chr6D 83.642 324 24 15 696 994 447760779 447761098 8.040000e-71 278.0
18 TraesCS6A01G366100 chr6D 87.554 233 23 3 179 409 446947776 446948004 6.260000e-67 265.0
19 TraesCS6A01G366100 chr6D 86.184 152 13 4 34 185 447760383 447760526 1.090000e-34 158.0
20 TraesCS6A01G366100 chr6D 83.626 171 17 7 206 374 446929820 446929981 1.830000e-32 150.0
21 TraesCS6A01G366100 chr6D 81.208 149 15 4 2017 2158 446726201 446726059 1.120000e-19 108.0
22 TraesCS6A01G366100 chr6D 85.714 70 4 4 362 425 446728786 446728717 5.270000e-08 69.4
23 TraesCS6A01G366100 chr6B 82.550 1106 91 44 1264 2336 676730539 676729503 0.000000e+00 880.0
24 TraesCS6A01G366100 chr6B 86.016 851 78 22 922 1755 676492804 676491978 0.000000e+00 874.0
25 TraesCS6A01G366100 chr6B 81.222 1129 130 54 936 2024 677045708 677044622 0.000000e+00 835.0
26 TraesCS6A01G366100 chr6B 85.307 667 56 23 883 1537 676538445 676537809 0.000000e+00 651.0
27 TraesCS6A01G366100 chr6B 78.540 904 115 47 1409 2277 678357367 678358226 3.370000e-144 521.0
28 TraesCS6A01G366100 chr6B 79.379 805 95 38 1408 2171 678175099 678175873 4.380000e-138 501.0
29 TraesCS6A01G366100 chr6B 86.325 468 35 19 1888 2336 676536785 676536328 1.590000e-132 483.0
30 TraesCS6A01G366100 chr6B 79.361 751 88 44 1312 2024 677336684 677335963 1.600000e-127 466.0
31 TraesCS6A01G366100 chr6B 85.371 458 46 13 953 1402 676865932 676865488 3.460000e-124 455.0
32 TraesCS6A01G366100 chr6B 83.148 540 43 24 1811 2336 676491961 676491456 1.610000e-122 449.0
33 TraesCS6A01G366100 chr6B 82.239 518 63 20 895 1401 677088456 677087957 1.260000e-113 420.0
34 TraesCS6A01G366100 chr6B 83.195 482 48 18 924 1402 678174606 678175057 7.600000e-111 411.0
35 TraesCS6A01G366100 chr6B 77.388 827 77 40 193 932 676373148 676372345 9.900000e-105 390.0
36 TraesCS6A01G366100 chr6B 80.791 531 46 31 1403 1915 678092355 678091863 6.000000e-97 364.0
37 TraesCS6A01G366100 chr6B 77.544 570 71 37 1756 2277 677087685 677087125 1.030000e-74 291.0
38 TraesCS6A01G366100 chr6B 80.310 452 25 22 34 463 676731585 676731176 1.730000e-72 283.0
39 TraesCS6A01G366100 chr6B 79.157 451 31 26 34 463 676499018 676498610 1.360000e-63 254.0
40 TraesCS6A01G366100 chr6B 85.593 236 24 5 179 409 675569203 675568973 3.800000e-59 239.0
41 TraesCS6A01G366100 chr6B 81.366 322 24 7 2288 2576 676729519 676729201 2.280000e-56 230.0
42 TraesCS6A01G366100 chr6B 80.000 345 35 16 137 461 678540357 678540687 1.060000e-54 224.0
43 TraesCS6A01G366100 chr6B 80.508 236 17 13 2296 2505 676491465 676491233 1.410000e-33 154.0
44 TraesCS6A01G366100 chr6B 89.344 122 6 3 698 819 676730974 676730860 2.370000e-31 147.0
45 TraesCS6A01G366100 chr6B 81.884 138 13 7 296 425 675627689 675627556 4.020000e-19 106.0
46 TraesCS6A01G366100 chr6B 87.500 88 10 1 2846 2933 676728499 676728413 1.870000e-17 100.0
47 TraesCS6A01G366100 chr6B 87.952 83 6 2 722 804 678093055 678092977 8.700000e-16 95.3
48 TraesCS6A01G366100 chr6B 93.333 60 4 0 2735 2794 713938436 713938377 4.050000e-14 89.8
49 TraesCS6A01G366100 chr6B 79.021 143 17 8 640 777 677337238 677337104 5.230000e-13 86.1
50 TraesCS6A01G366100 chr6B 88.571 70 4 2 731 800 677088554 677088489 6.770000e-12 82.4
51 TraesCS6A01G366100 chr6B 92.857 56 4 0 722 777 678356666 678356721 6.770000e-12 82.4
52 TraesCS6A01G366100 chr5A 79.407 675 74 31 991 1659 637061149 637061764 1.630000e-112 416.0
53 TraesCS6A01G366100 chr5A 93.548 62 3 1 2731 2791 657987088 657987027 1.120000e-14 91.6
54 TraesCS6A01G366100 chr7A 81.025 527 46 30 1848 2336 19012987 19013497 1.290000e-98 370.0
55 TraesCS6A01G366100 chr7A 92.063 63 5 0 2733 2795 717938590 717938652 4.050000e-14 89.8
56 TraesCS6A01G366100 chr4B 95.312 64 3 0 2732 2795 562355661 562355724 5.200000e-18 102.0
57 TraesCS6A01G366100 chr4D 95.082 61 3 0 2735 2795 323605979 323606039 2.420000e-16 97.1
58 TraesCS6A01G366100 chr7D 92.424 66 4 1 2730 2795 32015244 32015180 3.130000e-15 93.5
59 TraesCS6A01G366100 chr3B 91.935 62 5 0 2734 2795 127932636 127932697 1.460000e-13 87.9
60 TraesCS6A01G366100 chr1A 93.333 60 3 1 2734 2793 30182772 30182714 1.460000e-13 87.9
61 TraesCS6A01G366100 chr2B 91.803 61 5 0 2735 2795 779340578 779340638 5.230000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G366100 chr6A 593928024 593930970 2946 True 5443.000000 5443 100.000000 1 2947 1 chr6A.!!$R2 2946
1 TraesCS6A01G366100 chr6A 569678293 569679082 789 True 649.000000 649 81.786000 1048 1878 1 chr6A.!!$R1 830
2 TraesCS6A01G366100 chr6A 593991156 593992011 855 True 512.000000 512 78.436000 1398 2254 1 chr6A.!!$R3 856
3 TraesCS6A01G366100 chr6A 594319147 594320413 1266 False 355.500000 411 78.272000 930 2164 2 chr6A.!!$F2 1234
4 TraesCS6A01G366100 chr6A 594253212 594254308 1096 True 350.500000 381 79.518000 956 2069 2 chr6A.!!$R4 1113
5 TraesCS6A01G366100 chr6A 594364283 594366942 2659 False 212.125000 320 85.470750 88 2336 4 chr6A.!!$F3 2248
6 TraesCS6A01G366100 chr6D 447212935 447216494 3559 True 758.000000 1068 81.232500 34 1904 2 chr6D.!!$R3 1870
7 TraesCS6A01G366100 chr6D 447760383 447762213 1830 False 469.333333 972 84.251000 34 2163 3 chr6D.!!$F4 2129
8 TraesCS6A01G366100 chr6D 447278480 447279199 719 True 468.000000 468 79.079000 678 1417 1 chr6D.!!$R1 739
9 TraesCS6A01G366100 chr6B 677044622 677045708 1086 True 835.000000 835 81.222000 936 2024 1 chr6B.!!$R6 1088
10 TraesCS6A01G366100 chr6B 676536328 676538445 2117 True 567.000000 651 85.816000 883 2336 2 chr6B.!!$R9 1453
11 TraesCS6A01G366100 chr6B 676491233 676492804 1571 True 492.333333 874 83.224000 922 2505 3 chr6B.!!$R8 1583
12 TraesCS6A01G366100 chr6B 678174606 678175873 1267 False 456.000000 501 81.287000 924 2171 2 chr6B.!!$F2 1247
13 TraesCS6A01G366100 chr6B 676372345 676373148 803 True 390.000000 390 77.388000 193 932 1 chr6B.!!$R3 739
14 TraesCS6A01G366100 chr6B 676728413 676731585 3172 True 328.000000 880 84.214000 34 2933 5 chr6B.!!$R10 2899
15 TraesCS6A01G366100 chr6B 678356666 678358226 1560 False 301.700000 521 85.698500 722 2277 2 chr6B.!!$F3 1555
16 TraesCS6A01G366100 chr6B 677335963 677337238 1275 True 276.050000 466 79.191000 640 2024 2 chr6B.!!$R12 1384
17 TraesCS6A01G366100 chr6B 677087125 677088554 1429 True 264.466667 420 82.784667 731 2277 3 chr6B.!!$R11 1546
18 TraesCS6A01G366100 chr6B 678091863 678093055 1192 True 229.650000 364 84.371500 722 1915 2 chr6B.!!$R13 1193
19 TraesCS6A01G366100 chr5A 637061149 637061764 615 False 416.000000 416 79.407000 991 1659 1 chr5A.!!$F1 668
20 TraesCS6A01G366100 chr7A 19012987 19013497 510 False 370.000000 370 81.025000 1848 2336 1 chr7A.!!$F1 488

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
620 2324 0.39034 TGCATCAGTGAAGACGCTCC 60.39 55.0 0.0 0.0 34.38 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 5554 0.107508 CAAGATGGTGGCCTGATCGT 60.108 55.0 3.32 0.0 0.0 3.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.323477 CCGGCCCTTCACGGTGAA 62.323 66.667 21.30 21.30 44.85 3.18
19 20 2.281208 CGGCCCTTCACGGTGAAA 60.281 61.111 22.60 8.54 35.73 2.69
20 21 1.894756 CGGCCCTTCACGGTGAAAA 60.895 57.895 22.60 3.78 35.73 2.29
21 22 1.241315 CGGCCCTTCACGGTGAAAAT 61.241 55.000 22.60 0.00 35.73 1.82
22 23 1.828979 GGCCCTTCACGGTGAAAATA 58.171 50.000 22.60 2.70 35.73 1.40
23 24 1.471287 GGCCCTTCACGGTGAAAATAC 59.529 52.381 22.60 12.88 35.73 1.89
24 25 2.156098 GCCCTTCACGGTGAAAATACA 58.844 47.619 22.60 1.61 35.73 2.29
25 26 2.095415 GCCCTTCACGGTGAAAATACAC 60.095 50.000 22.60 7.42 35.73 2.90
59 60 1.607801 GCCACCCAATGAAGAAGGCC 61.608 60.000 0.00 0.00 34.71 5.19
77 78 1.880027 GCCAAAGTGAAACGGAGACAT 59.120 47.619 0.00 0.00 45.86 3.06
114 115 2.807895 CGGCCACGTTCGTTCGAT 60.808 61.111 2.24 0.00 34.81 3.59
115 116 2.785105 CGGCCACGTTCGTTCGATC 61.785 63.158 2.24 0.00 34.81 3.69
116 117 2.687436 GCCACGTTCGTTCGATCG 59.313 61.111 19.23 19.23 34.64 3.69
117 118 2.687436 CCACGTTCGTTCGATCGC 59.313 61.111 20.27 0.00 32.55 4.58
290 297 1.066858 GGGAGCGACTGAACAGATTCA 60.067 52.381 8.87 0.00 42.73 2.57
309 316 4.498520 CGAGCGCCGATGGACACT 62.499 66.667 2.29 0.00 41.76 3.55
478 531 1.131638 TCAGGTCCTTTCAGTGTGCT 58.868 50.000 0.00 0.00 0.00 4.40
480 533 0.536006 AGGTCCTTTCAGTGTGCTGC 60.536 55.000 0.00 0.00 42.29 5.25
482 535 0.590195 GTCCTTTCAGTGTGCTGCAG 59.410 55.000 10.11 10.11 42.29 4.41
491 544 0.941542 GTGTGCTGCAGACGGTTTAA 59.058 50.000 20.43 0.00 0.00 1.52
532 593 2.671619 ACAACCGGTGGGATTGCG 60.672 61.111 15.05 0.00 36.97 4.85
542 604 2.799978 GGTGGGATTGCGAAACAAAAAG 59.200 45.455 0.00 0.00 42.86 2.27
548 611 5.276820 GGGATTGCGAAACAAAAAGAAGTTG 60.277 40.000 0.00 0.00 42.86 3.16
559 622 1.247567 AAGAAGTTGGACATTGCCCG 58.752 50.000 0.00 0.00 0.00 6.13
567 630 0.746563 GGACATTGCCCGATTTCCGA 60.747 55.000 0.00 0.00 41.76 4.55
568 631 0.657840 GACATTGCCCGATTTCCGAG 59.342 55.000 0.00 0.00 41.76 4.63
587 651 3.737172 GAACCGGCACATGCGCTT 61.737 61.111 9.73 0.00 43.26 4.68
597 674 3.489059 GGCACATGCGCTTTGTAATATGT 60.489 43.478 9.73 4.23 43.26 2.29
620 2324 0.390340 TGCATCAGTGAAGACGCTCC 60.390 55.000 0.00 0.00 34.38 4.70
628 2339 2.094286 AGTGAAGACGCTCCTGATGAAG 60.094 50.000 0.00 0.00 30.39 3.02
778 2556 6.547141 ACCAGAATTTTGACACTGAAATCAGA 59.453 34.615 16.93 0.00 46.59 3.27
853 2688 2.837326 AACCCAAGACCGGTTCCCC 61.837 63.158 9.42 0.00 39.46 4.81
856 2691 2.526046 CCAAGACCGGTTCCCCTGT 61.526 63.158 9.42 0.00 0.00 4.00
858 2693 3.192103 AAGACCGGTTCCCCTGTGC 62.192 63.158 9.42 0.00 0.00 4.57
859 2694 3.637273 GACCGGTTCCCCTGTGCT 61.637 66.667 9.42 0.00 0.00 4.40
860 2695 2.203877 ACCGGTTCCCCTGTGCTA 60.204 61.111 0.00 0.00 0.00 3.49
861 2696 2.267961 CCGGTTCCCCTGTGCTAC 59.732 66.667 0.00 0.00 0.00 3.58
862 2697 2.267961 CGGTTCCCCTGTGCTACC 59.732 66.667 0.00 0.00 0.00 3.18
863 2698 2.291043 CGGTTCCCCTGTGCTACCT 61.291 63.158 0.00 0.00 0.00 3.08
864 2699 1.299976 GGTTCCCCTGTGCTACCTG 59.700 63.158 0.00 0.00 0.00 4.00
865 2700 1.377333 GTTCCCCTGTGCTACCTGC 60.377 63.158 0.00 0.00 43.25 4.85
924 3175 0.875059 GAACTGCAGGTTTTCTCCGG 59.125 55.000 19.93 0.00 38.41 5.14
934 3186 2.483106 GGTTTTCTCCGGCACTAAGTTC 59.517 50.000 0.00 0.00 0.00 3.01
949 3201 0.981943 AGTTCCCAAACTACCCCTCG 59.018 55.000 0.00 0.00 43.98 4.63
954 3207 1.338769 CCCAAACTACCCCTCGTTCTG 60.339 57.143 0.00 0.00 0.00 3.02
1052 3338 6.025749 TCAACTCACTACTCACATACCAAG 57.974 41.667 0.00 0.00 0.00 3.61
1075 3369 3.373830 CCACTCCTCTTCTCTGATTCCT 58.626 50.000 0.00 0.00 0.00 3.36
1110 3441 2.103094 CCCTCGTCTAATCTCAATGGCA 59.897 50.000 0.00 0.00 0.00 4.92
1231 3626 2.805353 CGGTCAAGTCCGTCAGCG 60.805 66.667 0.00 0.00 44.77 5.18
1232 3627 3.112709 GGTCAAGTCCGTCAGCGC 61.113 66.667 0.00 0.00 36.67 5.92
1233 3628 3.112709 GTCAAGTCCGTCAGCGCC 61.113 66.667 2.29 0.00 36.67 6.53
1234 3629 4.373116 TCAAGTCCGTCAGCGCCC 62.373 66.667 2.29 0.00 36.67 6.13
1235 3630 4.379243 CAAGTCCGTCAGCGCCCT 62.379 66.667 2.29 0.00 36.67 5.19
1236 3631 4.379243 AAGTCCGTCAGCGCCCTG 62.379 66.667 2.29 0.00 40.54 4.45
1240 3635 4.803426 CCGTCAGCGCCCTGTCTC 62.803 72.222 2.29 0.00 40.09 3.36
1241 3636 4.803426 CGTCAGCGCCCTGTCTCC 62.803 72.222 2.29 0.00 40.09 3.71
1242 3637 4.459089 GTCAGCGCCCTGTCTCCC 62.459 72.222 2.29 0.00 40.09 4.30
1262 3657 3.465403 CTCCTCTCCCGTGGGCAG 61.465 72.222 0.00 0.00 34.68 4.85
1338 3733 2.192861 CCGTTGCAGCCTCCACAAA 61.193 57.895 0.00 0.00 0.00 2.83
1582 4515 2.044352 TCTCCGGCGTCTCCATGA 60.044 61.111 6.01 0.00 34.01 3.07
1586 4519 3.822192 CGGCGTCTCCATGACCGA 61.822 66.667 0.00 0.00 42.49 4.69
1625 4570 6.039616 GCATTAACCAGTGAAAAGACAACAA 58.960 36.000 0.00 0.00 0.00 2.83
1638 4583 1.154672 CAACAACGTCGACATGCCG 60.155 57.895 17.16 3.32 0.00 5.69
1660 4616 6.144080 GCCGTAGCAAAGATACAAGTACATAG 59.856 42.308 0.00 0.00 39.53 2.23
1669 4625 7.596749 AGATACAAGTACATAGTGCACAAAC 57.403 36.000 21.04 9.08 0.00 2.93
1670 4626 7.386851 AGATACAAGTACATAGTGCACAAACT 58.613 34.615 21.04 11.22 0.00 2.66
1671 4627 5.673337 ACAAGTACATAGTGCACAAACTG 57.327 39.130 21.04 12.41 0.00 3.16
1672 4628 5.123227 ACAAGTACATAGTGCACAAACTGT 58.877 37.500 21.04 17.26 0.00 3.55
1673 4629 5.588648 ACAAGTACATAGTGCACAAACTGTT 59.411 36.000 21.04 0.00 0.00 3.16
1674 4630 5.924475 AGTACATAGTGCACAAACTGTTC 57.076 39.130 21.04 13.19 0.00 3.18
1677 4633 4.968259 ACATAGTGCACAAACTGTTCCTA 58.032 39.130 21.04 0.00 0.00 2.94
1860 5138 2.243264 GCTCCGCTGCACATAGAGC 61.243 63.158 0.00 5.25 42.74 4.09
1867 5145 1.470632 GCTGCACATAGAGCGACTTCT 60.471 52.381 0.00 0.00 33.85 2.85
1916 5207 1.752694 GCTCTCGTCCTCTCTGCCT 60.753 63.158 0.00 0.00 0.00 4.75
1923 5214 1.760086 TCCTCTCTGCCTGCTAGCC 60.760 63.158 13.29 0.00 0.00 3.93
1932 5223 1.483004 TGCCTGCTAGCCGTGTATAAA 59.517 47.619 13.29 0.00 0.00 1.40
1944 5240 5.708230 AGCCGTGTATAAACCTTGATTTTGA 59.292 36.000 0.00 0.00 0.00 2.69
1972 5276 6.687604 TGGATATACATCAATACGTGAGTGG 58.312 40.000 0.00 0.00 40.43 4.00
2078 5418 1.946768 TGCTTCCGTTTCTGTTTCTGG 59.053 47.619 0.00 0.00 0.00 3.86
2079 5419 2.218603 GCTTCCGTTTCTGTTTCTGGA 58.781 47.619 0.00 0.00 0.00 3.86
2080 5420 2.224314 GCTTCCGTTTCTGTTTCTGGAG 59.776 50.000 0.00 0.00 0.00 3.86
2081 5421 3.467803 CTTCCGTTTCTGTTTCTGGAGT 58.532 45.455 0.00 0.00 0.00 3.85
2082 5422 4.628074 CTTCCGTTTCTGTTTCTGGAGTA 58.372 43.478 0.00 0.00 0.00 2.59
2083 5423 4.884668 TCCGTTTCTGTTTCTGGAGTAT 57.115 40.909 0.00 0.00 0.00 2.12
2104 5453 0.620556 ATGCATCTCCCCTGTTTCGT 59.379 50.000 0.00 0.00 0.00 3.85
2238 5616 0.319641 ACTCCGGCGAAGTTTCTGTC 60.320 55.000 9.30 0.00 0.00 3.51
2260 5647 2.472059 TTTCATGGCGCGGCTGATC 61.472 57.895 33.23 1.82 0.00 2.92
2306 5696 6.961554 CCTGCTCGTGATATTTTTACTGTTTC 59.038 38.462 0.00 0.00 0.00 2.78
2338 5756 9.665264 GAGAAAGTGGTTTATTTTACTGTTGAG 57.335 33.333 0.00 0.00 0.00 3.02
2341 5759 5.048991 AGTGGTTTATTTTACTGTTGAGCGG 60.049 40.000 0.00 0.00 0.00 5.52
2366 5784 4.547367 CGGAGCGGTTGGGATCCC 62.547 72.222 25.22 25.22 39.32 3.85
2441 5888 2.519013 GGTTCTGTTTCTTGGCCAGAT 58.481 47.619 5.11 0.00 35.32 2.90
2450 5897 4.842531 TTCTTGGCCAGATATCAGTTGA 57.157 40.909 5.11 0.00 0.00 3.18
2451 5898 5.378230 TTCTTGGCCAGATATCAGTTGAT 57.622 39.130 5.11 0.00 38.51 2.57
2471 5918 1.871080 GGGCTCACCAATACTCATCG 58.129 55.000 0.00 0.00 39.85 3.84
2472 5919 1.221414 GGCTCACCAATACTCATCGC 58.779 55.000 0.00 0.00 35.26 4.58
2480 5933 2.614057 CCAATACTCATCGCCTTTGGAC 59.386 50.000 0.00 0.00 36.55 4.02
2511 5964 2.042464 TCTGTCAGTTGGCTCTTGTCT 58.958 47.619 0.00 0.00 0.00 3.41
2514 5967 2.965831 TGTCAGTTGGCTCTTGTCTACT 59.034 45.455 0.00 0.00 34.44 2.57
2515 5968 3.005897 TGTCAGTTGGCTCTTGTCTACTC 59.994 47.826 0.00 0.00 31.98 2.59
2518 5971 2.564947 AGTTGGCTCTTGTCTACTCTGG 59.435 50.000 0.00 0.00 28.35 3.86
2537 5990 0.515564 GAGTATTGCGTGCGGTGTTT 59.484 50.000 0.00 0.00 0.00 2.83
2592 6454 3.691118 CCTTTTCAGATGAGCGAATGGAA 59.309 43.478 0.00 0.00 0.00 3.53
2612 6474 5.106752 TGGAACGATGAACACACAATACATG 60.107 40.000 0.00 0.00 0.00 3.21
2613 6475 5.106712 GGAACGATGAACACACAATACATGT 60.107 40.000 2.69 2.69 45.34 3.21
2616 6478 7.609760 ACGATGAACACACAATACATGTTAT 57.390 32.000 2.30 0.00 41.46 1.89
2619 6481 5.626211 TGAACACACAATACATGTTATGCG 58.374 37.500 2.30 0.15 41.46 4.73
2621 6483 4.257731 ACACACAATACATGTTATGCGGA 58.742 39.130 2.30 0.00 41.46 5.54
2626 6488 4.095782 ACAATACATGTTATGCGGACAACC 59.904 41.667 2.30 0.00 40.06 3.77
2630 6492 2.192664 TGTTATGCGGACAACCATGT 57.807 45.000 0.00 0.00 44.25 3.21
2631 6493 1.809547 TGTTATGCGGACAACCATGTG 59.190 47.619 0.00 0.00 40.74 3.21
2632 6494 1.132262 GTTATGCGGACAACCATGTGG 59.868 52.381 0.00 0.00 40.74 4.17
2658 6520 2.543777 TCAGTAGCAAGCTTCCGTTT 57.456 45.000 0.00 0.00 0.00 3.60
2660 6522 3.323243 TCAGTAGCAAGCTTCCGTTTAC 58.677 45.455 0.00 0.00 0.00 2.01
2662 6524 3.684788 CAGTAGCAAGCTTCCGTTTACAT 59.315 43.478 0.00 0.00 0.00 2.29
2663 6525 4.868171 CAGTAGCAAGCTTCCGTTTACATA 59.132 41.667 0.00 0.00 0.00 2.29
2664 6526 5.523916 CAGTAGCAAGCTTCCGTTTACATAT 59.476 40.000 0.00 0.00 0.00 1.78
2665 6527 4.882671 AGCAAGCTTCCGTTTACATATG 57.117 40.909 0.00 0.00 0.00 1.78
2666 6528 3.065371 AGCAAGCTTCCGTTTACATATGC 59.935 43.478 1.58 0.00 0.00 3.14
2668 6530 2.901249 AGCTTCCGTTTACATATGCGT 58.099 42.857 1.58 0.00 0.00 5.24
2669 6531 4.049546 AGCTTCCGTTTACATATGCGTA 57.950 40.909 1.58 0.00 0.00 4.42
2670 6532 3.800506 AGCTTCCGTTTACATATGCGTAC 59.199 43.478 1.58 0.00 0.00 3.67
2671 6533 3.552699 GCTTCCGTTTACATATGCGTACA 59.447 43.478 1.58 0.00 0.00 2.90
2706 6568 0.235926 GAACAGCTGACAGGCGAAAC 59.764 55.000 23.35 0.00 37.29 2.78
2717 6579 1.228154 GGCGAAACCCAAGTGGAGT 60.228 57.895 0.00 0.00 37.39 3.85
2721 6583 1.692411 GAAACCCAAGTGGAGTTGCT 58.308 50.000 0.00 0.00 37.39 3.91
2732 6594 2.558359 GTGGAGTTGCTGGCAGTTTAAT 59.442 45.455 17.16 0.71 0.00 1.40
2733 6595 2.557924 TGGAGTTGCTGGCAGTTTAATG 59.442 45.455 17.16 0.00 0.00 1.90
2734 6596 2.558359 GGAGTTGCTGGCAGTTTAATGT 59.442 45.455 17.16 1.84 0.00 2.71
2735 6597 3.756434 GGAGTTGCTGGCAGTTTAATGTA 59.244 43.478 17.16 0.00 0.00 2.29
2736 6598 4.379499 GGAGTTGCTGGCAGTTTAATGTAC 60.379 45.833 17.16 3.34 0.00 2.90
2737 6599 4.398319 AGTTGCTGGCAGTTTAATGTACT 58.602 39.130 17.16 5.45 0.00 2.73
2738 6600 4.455877 AGTTGCTGGCAGTTTAATGTACTC 59.544 41.667 17.16 0.00 0.00 2.59
2739 6601 3.343617 TGCTGGCAGTTTAATGTACTCC 58.656 45.455 17.16 0.00 0.00 3.85
2740 6602 2.683362 GCTGGCAGTTTAATGTACTCCC 59.317 50.000 17.16 0.00 0.00 4.30
2742 6604 4.192317 CTGGCAGTTTAATGTACTCCCTC 58.808 47.826 6.28 0.00 0.00 4.30
2743 6605 3.054655 TGGCAGTTTAATGTACTCCCTCC 60.055 47.826 0.00 0.00 0.00 4.30
2744 6606 3.195661 GCAGTTTAATGTACTCCCTCCG 58.804 50.000 0.00 0.00 0.00 4.63
2746 6608 4.430908 CAGTTTAATGTACTCCCTCCGTC 58.569 47.826 0.00 0.00 0.00 4.79
2747 6609 3.450096 AGTTTAATGTACTCCCTCCGTCC 59.550 47.826 0.00 0.00 0.00 4.79
2748 6610 2.077687 TAATGTACTCCCTCCGTCCC 57.922 55.000 0.00 0.00 0.00 4.46
2749 6611 1.041447 AATGTACTCCCTCCGTCCCG 61.041 60.000 0.00 0.00 0.00 5.14
2750 6612 1.929860 ATGTACTCCCTCCGTCCCGA 61.930 60.000 0.00 0.00 0.00 5.14
2752 6614 0.754587 GTACTCCCTCCGTCCCGAAT 60.755 60.000 0.00 0.00 0.00 3.34
2753 6615 0.032813 TACTCCCTCCGTCCCGAATT 60.033 55.000 0.00 0.00 0.00 2.17
2754 6616 0.032813 ACTCCCTCCGTCCCGAATTA 60.033 55.000 0.00 0.00 0.00 1.40
2755 6617 0.388294 CTCCCTCCGTCCCGAATTAC 59.612 60.000 0.00 0.00 0.00 1.89
2756 6618 0.032813 TCCCTCCGTCCCGAATTACT 60.033 55.000 0.00 0.00 0.00 2.24
2757 6619 0.828677 CCCTCCGTCCCGAATTACTT 59.171 55.000 0.00 0.00 0.00 2.24
2758 6620 1.472728 CCCTCCGTCCCGAATTACTTG 60.473 57.143 0.00 0.00 0.00 3.16
2759 6621 1.206371 CCTCCGTCCCGAATTACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
2760 6622 2.537401 CTCCGTCCCGAATTACTTGTC 58.463 52.381 0.00 0.00 0.00 3.18
2761 6623 1.135315 TCCGTCCCGAATTACTTGTCG 60.135 52.381 0.00 0.00 37.01 4.35
2762 6624 0.643820 CGTCCCGAATTACTTGTCGC 59.356 55.000 0.00 0.00 35.93 5.19
2763 6625 1.717194 GTCCCGAATTACTTGTCGCA 58.283 50.000 0.00 0.00 35.93 5.10
2764 6626 1.392510 GTCCCGAATTACTTGTCGCAC 59.607 52.381 0.00 0.00 35.93 5.34
2765 6627 1.001068 TCCCGAATTACTTGTCGCACA 59.999 47.619 0.00 0.00 35.93 4.57
2766 6628 1.801771 CCCGAATTACTTGTCGCACAA 59.198 47.619 2.49 2.49 36.54 3.33
2767 6629 2.224549 CCCGAATTACTTGTCGCACAAA 59.775 45.455 3.84 0.00 37.69 2.83
2768 6630 3.119990 CCCGAATTACTTGTCGCACAAAT 60.120 43.478 3.84 0.00 37.69 2.32
2769 6631 3.845775 CCGAATTACTTGTCGCACAAATG 59.154 43.478 3.84 0.00 37.69 2.32
2770 6632 4.377943 CCGAATTACTTGTCGCACAAATGA 60.378 41.667 3.84 0.00 37.69 2.57
2771 6633 5.143660 CGAATTACTTGTCGCACAAATGAA 58.856 37.500 3.84 0.33 37.69 2.57
2772 6634 5.794945 CGAATTACTTGTCGCACAAATGAAT 59.205 36.000 3.84 2.11 37.69 2.57
2773 6635 6.958752 CGAATTACTTGTCGCACAAATGAATA 59.041 34.615 3.84 0.00 37.69 1.75
2774 6636 7.480229 CGAATTACTTGTCGCACAAATGAATAA 59.520 33.333 3.84 0.00 37.69 1.40
2775 6637 9.123709 GAATTACTTGTCGCACAAATGAATAAA 57.876 29.630 3.84 0.00 37.69 1.40
2776 6638 9.469807 AATTACTTGTCGCACAAATGAATAAAA 57.530 25.926 3.84 0.00 37.69 1.52
2777 6639 8.858003 TTACTTGTCGCACAAATGAATAAAAA 57.142 26.923 3.84 0.00 37.69 1.94
2778 6640 7.945033 ACTTGTCGCACAAATGAATAAAAAT 57.055 28.000 3.84 0.00 37.69 1.82
2779 6641 8.006741 ACTTGTCGCACAAATGAATAAAAATC 57.993 30.769 3.84 0.00 37.69 2.17
2780 6642 6.609907 TGTCGCACAAATGAATAAAAATCG 57.390 33.333 0.00 0.00 0.00 3.34
2781 6643 6.374578 TGTCGCACAAATGAATAAAAATCGA 58.625 32.000 0.00 0.00 0.00 3.59
2782 6644 7.026562 TGTCGCACAAATGAATAAAAATCGAT 58.973 30.769 0.00 0.00 0.00 3.59
2783 6645 7.008176 TGTCGCACAAATGAATAAAAATCGATG 59.992 33.333 0.00 0.00 0.00 3.84
2784 6646 7.008266 GTCGCACAAATGAATAAAAATCGATGT 59.992 33.333 0.00 0.00 0.00 3.06
2785 6647 8.178313 TCGCACAAATGAATAAAAATCGATGTA 58.822 29.630 0.00 0.00 0.00 2.29
2786 6648 8.957028 CGCACAAATGAATAAAAATCGATGTAT 58.043 29.630 0.00 0.00 0.00 2.29
2796 6658 9.930693 AATAAAAATCGATGTATCTAGGACTCC 57.069 33.333 0.00 0.00 0.00 3.85
2805 6667 8.744652 CGATGTATCTAGGACTCCTTGAATATT 58.255 37.037 12.55 0.48 38.69 1.28
2862 6791 0.582005 GTCAGGTCAACAGAACGCAC 59.418 55.000 0.00 0.00 0.00 5.34
2868 6797 2.660552 AACAGAACGCACGACCCG 60.661 61.111 0.00 0.00 0.00 5.28
2880 6809 1.590792 CGACCCGGCGGAATAACTC 60.591 63.158 30.79 10.24 0.00 3.01
2884 6813 0.666577 CCCGGCGGAATAACTCGATC 60.667 60.000 30.79 0.00 0.00 3.69
2893 6822 1.409412 ATAACTCGATCGCGACATGC 58.591 50.000 12.93 0.00 42.51 4.06
2928 6857 2.506472 GGAGGCCGGACTTGATCC 59.494 66.667 13.62 3.73 45.20 3.36
2935 6864 3.400007 GGACTTGATCCGCGCTTC 58.600 61.111 5.56 0.00 37.88 3.86
2936 6865 2.174319 GGACTTGATCCGCGCTTCC 61.174 63.158 5.56 0.00 37.88 3.46
2937 6866 1.447838 GACTTGATCCGCGCTTCCA 60.448 57.895 5.56 0.00 0.00 3.53
2938 6867 1.003839 ACTTGATCCGCGCTTCCAA 60.004 52.632 5.56 3.57 0.00 3.53
2939 6868 0.605319 ACTTGATCCGCGCTTCCAAA 60.605 50.000 5.56 0.00 0.00 3.28
2940 6869 0.097674 CTTGATCCGCGCTTCCAAAG 59.902 55.000 5.56 0.00 0.00 2.77
2941 6870 1.305219 TTGATCCGCGCTTCCAAAGG 61.305 55.000 5.56 0.00 0.00 3.11
2942 6871 2.438434 ATCCGCGCTTCCAAAGGG 60.438 61.111 5.56 0.00 43.66 3.95
2943 6872 3.268103 ATCCGCGCTTCCAAAGGGT 62.268 57.895 5.56 0.00 42.85 4.34
2944 6873 2.764637 ATCCGCGCTTCCAAAGGGTT 62.765 55.000 5.56 0.00 42.85 4.11
2945 6874 2.561373 CGCGCTTCCAAAGGGTTC 59.439 61.111 5.56 0.00 42.85 3.62
2946 6875 2.561373 GCGCTTCCAAAGGGTTCG 59.439 61.111 0.00 0.00 42.85 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.095415 GTGTATTTTCACCGTGAAGGGC 60.095 50.000 13.51 7.03 46.96 5.19
14 15 2.095415 GCTTCGGTGGGTGTATTTTCAC 60.095 50.000 0.00 0.00 37.57 3.18
16 17 1.129811 CGCTTCGGTGGGTGTATTTTC 59.870 52.381 0.00 0.00 0.00 2.29
17 18 1.161843 CGCTTCGGTGGGTGTATTTT 58.838 50.000 0.00 0.00 0.00 1.82
18 19 1.303091 GCGCTTCGGTGGGTGTATTT 61.303 55.000 0.00 0.00 0.00 1.40
19 20 1.743995 GCGCTTCGGTGGGTGTATT 60.744 57.895 0.00 0.00 0.00 1.89
20 21 2.125269 GCGCTTCGGTGGGTGTAT 60.125 61.111 0.00 0.00 0.00 2.29
21 22 4.728102 CGCGCTTCGGTGGGTGTA 62.728 66.667 5.56 0.00 34.35 2.90
59 60 3.138304 TCCATGTCTCCGTTTCACTTTG 58.862 45.455 0.00 0.00 0.00 2.77
77 78 1.004560 CTCTTTCGCTGCCACTCCA 60.005 57.895 0.00 0.00 0.00 3.86
113 114 4.129737 CGACCCACACGAGGCGAT 62.130 66.667 0.00 0.00 0.00 4.58
155 156 1.132588 GATGCTCCGATCGCTGTTAC 58.867 55.000 10.32 0.00 0.00 2.50
226 227 2.106683 CCGCGCGAAGGAAGGAATT 61.107 57.895 34.63 0.00 0.00 2.17
309 316 2.267426 CATCTGTCGTCGTAATGGCAA 58.733 47.619 0.00 0.00 0.00 4.52
478 531 1.804151 GCTGTCATTAAACCGTCTGCA 59.196 47.619 0.00 0.00 0.00 4.41
480 533 3.664276 CGTTGCTGTCATTAAACCGTCTG 60.664 47.826 0.00 0.00 0.00 3.51
482 535 2.222445 ACGTTGCTGTCATTAAACCGTC 59.778 45.455 0.00 0.00 0.00 4.79
491 544 1.100463 TTGTGCCACGTTGCTGTCAT 61.100 50.000 13.27 0.00 0.00 3.06
532 593 6.456853 GGCAATGTCCAACTTCTTTTTGTTTC 60.457 38.462 0.00 0.00 0.00 2.78
542 604 1.463674 ATCGGGCAATGTCCAACTTC 58.536 50.000 4.21 0.00 0.00 3.01
548 611 0.746563 TCGGAAATCGGGCAATGTCC 60.747 55.000 0.00 0.00 39.77 4.02
620 2324 7.757173 TGATTCGTAACTTTCTCTCTTCATCAG 59.243 37.037 0.00 0.00 0.00 2.90
628 2339 4.030753 CGCACTGATTCGTAACTTTCTCTC 59.969 45.833 0.00 0.00 0.00 3.20
682 2421 8.289939 TGTCAAAGGAGTAGTATATTCGAACT 57.710 34.615 0.00 0.00 0.00 3.01
699 2448 7.445121 TGCTCCTATTATAGTCATGTCAAAGG 58.555 38.462 0.00 0.00 0.00 3.11
735 2506 6.258230 TCTGGTCAATTTCTTGCATTACAG 57.742 37.500 0.00 0.00 32.11 2.74
778 2556 5.275067 TGCCAACTTGCTTTGAAATACTT 57.725 34.783 0.00 0.00 0.00 2.24
858 2693 2.633481 GAGGTTATGGGTAGGCAGGTAG 59.367 54.545 0.00 0.00 0.00 3.18
859 2694 2.022820 TGAGGTTATGGGTAGGCAGGTA 60.023 50.000 0.00 0.00 0.00 3.08
860 2695 1.274184 TGAGGTTATGGGTAGGCAGGT 60.274 52.381 0.00 0.00 0.00 4.00
861 2696 1.417890 CTGAGGTTATGGGTAGGCAGG 59.582 57.143 0.00 0.00 0.00 4.85
862 2697 2.119495 ACTGAGGTTATGGGTAGGCAG 58.881 52.381 0.00 0.00 0.00 4.85
863 2698 2.263895 ACTGAGGTTATGGGTAGGCA 57.736 50.000 0.00 0.00 0.00 4.75
864 2699 3.710165 ACTAACTGAGGTTATGGGTAGGC 59.290 47.826 0.00 0.00 37.30 3.93
865 2700 5.952347 AACTAACTGAGGTTATGGGTAGG 57.048 43.478 0.00 0.00 37.30 3.18
924 3175 3.079578 GGGTAGTTTGGGAACTTAGTGC 58.920 50.000 0.00 0.00 43.48 4.40
934 3186 0.981943 AGAACGAGGGGTAGTTTGGG 59.018 55.000 0.00 0.00 0.00 4.12
1038 3311 2.500098 GAGTGGCCTTGGTATGTGAGTA 59.500 50.000 3.32 0.00 0.00 2.59
1039 3312 1.279271 GAGTGGCCTTGGTATGTGAGT 59.721 52.381 3.32 0.00 0.00 3.41
1040 3313 1.407437 GGAGTGGCCTTGGTATGTGAG 60.407 57.143 3.32 0.00 0.00 3.51
1041 3314 0.618458 GGAGTGGCCTTGGTATGTGA 59.382 55.000 3.32 0.00 0.00 3.58
1042 3315 3.175133 GGAGTGGCCTTGGTATGTG 57.825 57.895 3.32 0.00 0.00 3.21
1052 3338 1.494960 ATCAGAGAAGAGGAGTGGCC 58.505 55.000 0.00 0.00 0.00 5.36
1094 3419 2.032178 GCCGTTGCCATTGAGATTAGAC 59.968 50.000 0.00 0.00 0.00 2.59
1181 3513 1.446966 GAGAGCTTGACACGGGAGC 60.447 63.158 0.00 0.00 36.68 4.70
1245 3640 3.465403 CTGCCCACGGGAGAGGAG 61.465 72.222 6.21 0.00 44.17 3.69
1604 4546 5.181622 ACGTTGTTGTCTTTTCACTGGTTAA 59.818 36.000 0.00 0.00 0.00 2.01
1605 4547 4.696402 ACGTTGTTGTCTTTTCACTGGTTA 59.304 37.500 0.00 0.00 0.00 2.85
1638 4583 7.491372 TGCACTATGTACTTGTATCTTTGCTAC 59.509 37.037 0.00 0.00 0.00 3.58
1650 4596 5.673337 ACAGTTTGTGCACTATGTACTTG 57.327 39.130 19.41 8.06 33.97 3.16
1652 4598 4.755123 GGAACAGTTTGTGCACTATGTACT 59.245 41.667 19.41 8.31 33.97 2.73
1660 4616 5.880054 ATGTATAGGAACAGTTTGTGCAC 57.120 39.130 10.75 10.75 31.70 4.57
1860 5138 1.134175 GGAGCAGAGAGGAAGAAGTCG 59.866 57.143 0.00 0.00 0.00 4.18
1863 5141 2.178580 AGTGGAGCAGAGAGGAAGAAG 58.821 52.381 0.00 0.00 0.00 2.85
1867 5145 1.722034 ACAAGTGGAGCAGAGAGGAA 58.278 50.000 0.00 0.00 0.00 3.36
1916 5207 3.196039 TCAAGGTTTATACACGGCTAGCA 59.804 43.478 18.24 0.00 0.00 3.49
1923 5214 9.277565 CAGAATCAAAATCAAGGTTTATACACG 57.722 33.333 0.00 0.00 0.00 4.49
1932 5223 9.872684 ATGTATATCCAGAATCAAAATCAAGGT 57.127 29.630 0.00 0.00 0.00 3.50
1944 5240 8.807118 ACTCACGTATTGATGTATATCCAGAAT 58.193 33.333 0.00 0.00 32.17 2.40
1965 5266 2.030805 GTGTCTCCAATTTGCCACTCAC 60.031 50.000 0.00 0.00 0.00 3.51
1972 5276 4.107622 GCATGTATGTGTCTCCAATTTGC 58.892 43.478 0.00 0.00 0.00 3.68
2078 5418 2.636893 ACAGGGGAGATGCATCATACTC 59.363 50.000 27.81 16.69 0.00 2.59
2079 5419 2.699160 ACAGGGGAGATGCATCATACT 58.301 47.619 27.81 16.52 0.00 2.12
2080 5420 3.498774 AACAGGGGAGATGCATCATAC 57.501 47.619 27.81 17.43 0.00 2.39
2081 5421 3.494924 CGAAACAGGGGAGATGCATCATA 60.495 47.826 27.81 0.00 0.00 2.15
2082 5422 2.747467 CGAAACAGGGGAGATGCATCAT 60.747 50.000 27.81 13.31 0.00 2.45
2083 5423 1.407299 CGAAACAGGGGAGATGCATCA 60.407 52.381 27.81 0.00 0.00 3.07
2178 5554 0.107508 CAAGATGGTGGCCTGATCGT 60.108 55.000 3.32 0.00 0.00 3.73
2238 5616 2.504681 GCCGCGCCATGAAACTTG 60.505 61.111 0.00 0.00 0.00 3.16
2277 5664 2.225068 AAATATCACGAGCAGGACGG 57.775 50.000 0.00 0.00 34.93 4.79
2323 5741 3.009253 TCCCCCGCTCAACAGTAAAATAA 59.991 43.478 0.00 0.00 0.00 1.40
2366 5784 1.586028 CGCAAGTTGATGGGTTGGG 59.414 57.895 7.16 0.00 0.00 4.12
2374 5795 3.076621 TCATCTTCTTGCGCAAGTTGAT 58.923 40.909 40.37 36.07 39.38 2.57
2441 5888 2.195727 TGGTGAGCCCATCAACTGATA 58.804 47.619 0.00 0.00 46.60 2.15
2450 5897 2.224378 CGATGAGTATTGGTGAGCCCAT 60.224 50.000 0.00 0.00 44.74 4.00
2451 5898 1.138859 CGATGAGTATTGGTGAGCCCA 59.861 52.381 0.00 0.00 43.27 5.36
2472 5919 2.361610 ATGGCGCCAGTCCAAAGG 60.362 61.111 35.36 0.00 37.13 3.11
2480 5933 2.046988 TGACAGACATGGCGCCAG 60.047 61.111 35.36 26.66 37.19 4.85
2511 5964 1.202256 CGCACGCAATACTCCAGAGTA 60.202 52.381 9.84 9.84 46.68 2.59
2514 5967 1.153647 CCGCACGCAATACTCCAGA 60.154 57.895 0.00 0.00 0.00 3.86
2515 5968 1.447838 ACCGCACGCAATACTCCAG 60.448 57.895 0.00 0.00 0.00 3.86
2518 5971 0.515564 AAACACCGCACGCAATACTC 59.484 50.000 0.00 0.00 0.00 2.59
2546 5999 2.485426 ACCGATACTTCTCGTTCGTCAA 59.515 45.455 0.00 0.00 36.93 3.18
2592 6454 5.940192 AACATGTATTGTGTGTTCATCGT 57.060 34.783 0.00 0.00 38.99 3.73
2612 6474 1.132262 CCACATGGTTGTCCGCATAAC 59.868 52.381 0.00 0.00 32.34 1.89
2613 6475 1.003696 TCCACATGGTTGTCCGCATAA 59.996 47.619 0.00 0.00 32.34 1.90
2616 6478 0.251121 ATTCCACATGGTTGTCCGCA 60.251 50.000 0.00 0.00 32.34 5.69
2619 6481 3.763360 TGATTCATTCCACATGGTTGTCC 59.237 43.478 0.00 0.00 32.34 4.02
2621 6483 4.410099 ACTGATTCATTCCACATGGTTGT 58.590 39.130 0.00 0.00 36.15 3.32
2626 6488 5.732528 GCTTGCTACTGATTCATTCCACATG 60.733 44.000 0.00 0.00 0.00 3.21
2630 6492 4.226427 AGCTTGCTACTGATTCATTCCA 57.774 40.909 0.00 0.00 0.00 3.53
2631 6493 4.036144 GGAAGCTTGCTACTGATTCATTCC 59.964 45.833 11.19 0.00 31.10 3.01
2632 6494 4.260538 CGGAAGCTTGCTACTGATTCATTC 60.261 45.833 16.42 0.00 31.10 2.67
2675 6537 1.061711 CAGCTGTTCAACGCATCTAGC 59.938 52.381 5.25 0.00 40.87 3.42
2676 6538 2.346847 GTCAGCTGTTCAACGCATCTAG 59.653 50.000 14.67 0.00 0.00 2.43
2677 6539 2.288763 TGTCAGCTGTTCAACGCATCTA 60.289 45.455 14.67 0.00 0.00 1.98
2678 6540 1.151668 GTCAGCTGTTCAACGCATCT 58.848 50.000 14.67 0.00 0.00 2.90
2706 6568 2.270986 GCCAGCAACTCCACTTGGG 61.271 63.158 0.00 0.00 35.41 4.12
2717 6579 3.756434 GGAGTACATTAAACTGCCAGCAA 59.244 43.478 0.00 0.00 29.78 3.91
2744 6606 1.392510 GTGCGACAAGTAATTCGGGAC 59.607 52.381 0.00 0.00 35.73 4.46
2746 6608 1.434555 TGTGCGACAAGTAATTCGGG 58.565 50.000 0.00 0.00 35.73 5.14
2747 6609 3.529634 TTTGTGCGACAAGTAATTCGG 57.470 42.857 0.00 0.00 39.53 4.30
2748 6610 4.707563 TCATTTGTGCGACAAGTAATTCG 58.292 39.130 0.00 0.00 39.53 3.34
2749 6611 8.667987 TTATTCATTTGTGCGACAAGTAATTC 57.332 30.769 0.00 0.00 39.53 2.17
2750 6612 9.469807 TTTTATTCATTTGTGCGACAAGTAATT 57.530 25.926 0.00 0.00 39.53 1.40
2752 6614 8.858003 TTTTTATTCATTTGTGCGACAAGTAA 57.142 26.923 0.00 0.00 39.53 2.24
2753 6615 9.123709 GATTTTTATTCATTTGTGCGACAAGTA 57.876 29.630 0.00 0.00 39.53 2.24
2754 6616 7.148983 CGATTTTTATTCATTTGTGCGACAAGT 60.149 33.333 0.00 0.00 39.53 3.16
2755 6617 7.060518 TCGATTTTTATTCATTTGTGCGACAAG 59.939 33.333 0.00 0.00 39.53 3.16
2756 6618 6.858478 TCGATTTTTATTCATTTGTGCGACAA 59.142 30.769 0.00 0.00 36.11 3.18
2757 6619 6.374578 TCGATTTTTATTCATTTGTGCGACA 58.625 32.000 0.00 0.00 0.00 4.35
2758 6620 6.846870 TCGATTTTTATTCATTTGTGCGAC 57.153 33.333 0.00 0.00 0.00 5.19
2759 6621 7.026562 ACATCGATTTTTATTCATTTGTGCGA 58.973 30.769 0.00 0.00 0.00 5.10
2760 6622 7.208379 ACATCGATTTTTATTCATTTGTGCG 57.792 32.000 0.00 0.00 0.00 5.34
2770 6632 9.930693 GGAGTCCTAGATACATCGATTTTTATT 57.069 33.333 0.41 0.00 0.00 1.40
2771 6633 9.315363 AGGAGTCCTAGATACATCGATTTTTAT 57.685 33.333 10.94 0.00 28.47 1.40
2772 6634 8.707796 AGGAGTCCTAGATACATCGATTTTTA 57.292 34.615 10.94 0.00 28.47 1.52
2773 6635 7.604657 AGGAGTCCTAGATACATCGATTTTT 57.395 36.000 10.94 0.00 28.47 1.94
2774 6636 7.287927 TCAAGGAGTCCTAGATACATCGATTTT 59.712 37.037 13.43 0.00 31.13 1.82
2775 6637 6.778069 TCAAGGAGTCCTAGATACATCGATTT 59.222 38.462 13.43 0.00 31.13 2.17
2776 6638 6.307776 TCAAGGAGTCCTAGATACATCGATT 58.692 40.000 13.43 0.00 31.13 3.34
2777 6639 5.882040 TCAAGGAGTCCTAGATACATCGAT 58.118 41.667 13.43 0.00 31.13 3.59
2778 6640 5.306114 TCAAGGAGTCCTAGATACATCGA 57.694 43.478 13.43 0.00 31.13 3.59
2779 6641 6.582677 ATTCAAGGAGTCCTAGATACATCG 57.417 41.667 13.43 0.00 31.13 3.84
2782 6644 9.434275 TCAAATATTCAAGGAGTCCTAGATACA 57.566 33.333 13.43 0.00 31.13 2.29
2783 6645 9.699703 GTCAAATATTCAAGGAGTCCTAGATAC 57.300 37.037 13.43 0.00 31.13 2.24
2784 6646 8.577296 CGTCAAATATTCAAGGAGTCCTAGATA 58.423 37.037 13.43 11.24 31.13 1.98
2785 6647 7.287927 TCGTCAAATATTCAAGGAGTCCTAGAT 59.712 37.037 13.43 9.37 31.13 1.98
2786 6648 6.605995 TCGTCAAATATTCAAGGAGTCCTAGA 59.394 38.462 13.43 1.53 31.13 2.43
2787 6649 6.697892 GTCGTCAAATATTCAAGGAGTCCTAG 59.302 42.308 13.43 0.00 31.13 3.02
2788 6650 6.570692 GTCGTCAAATATTCAAGGAGTCCTA 58.429 40.000 13.43 0.00 31.13 2.94
2789 6651 5.420409 GTCGTCAAATATTCAAGGAGTCCT 58.580 41.667 5.62 5.62 33.87 3.85
2790 6652 4.267928 CGTCGTCAAATATTCAAGGAGTCC 59.732 45.833 0.00 0.00 0.00 3.85
2791 6653 4.267928 CCGTCGTCAAATATTCAAGGAGTC 59.732 45.833 0.00 0.00 0.00 3.36
2796 6658 2.675844 TGCCCGTCGTCAAATATTCAAG 59.324 45.455 0.00 0.00 0.00 3.02
2805 6667 2.933878 AAGCAAGTGCCCGTCGTCAA 62.934 55.000 0.00 0.00 43.38 3.18
2862 6791 1.590792 GAGTTATTCCGCCGGGTCG 60.591 63.158 1.90 0.00 33.83 4.79
2868 6797 1.606350 CGCGATCGAGTTATTCCGCC 61.606 60.000 21.57 0.00 39.52 6.13
2923 6852 1.745115 CCTTTGGAAGCGCGGATCA 60.745 57.895 8.83 0.00 0.00 2.92
2925 6854 2.438434 CCCTTTGGAAGCGCGGAT 60.438 61.111 8.83 0.00 0.00 4.18
2928 6857 2.561373 GAACCCTTTGGAAGCGCG 59.439 61.111 0.00 0.00 34.81 6.86
2929 6858 2.561373 CGAACCCTTTGGAAGCGC 59.439 61.111 0.00 0.00 34.81 5.92


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.